1 Introduction

Double strand breaks (DSBs) are a form of DNA damage that results in the loss of bases on both strands of the DNA helix. They are commonly repaired by the non-homologous end-joining (NHEJ) pathway, which requires the protein Ku. Ku is a heterodimer of Ku70/Ku80 subunits. It identifies and binds to DSBs prior to NHEJ, and takes part in some transposition events (d’Adda di Fagagna, Weller, Doherty, et al., 2003). Homologues of Ku have been found in many bacteria. The most well- known homologue of Ku is the Gam protein of the Mu bacteriophage.

Mu is a temperate bacteriophage of Enterobacteria, particularly Escherichia coli. In bacteria, Mu acts as a transposable element (Fuller and Rice, 2017) – meaning it can change its position within the genome and replicate by forming two replication forks (Shapiro, 1979). The Mu transposon involves 3 proteins: MuA, MuB, and MuGam (d’Adda di Fagagna, Weller, Doherty, et al., 2003; Fuller and Rice, 2017). MuB polymerises adjacent to the E. coli target site and associates with MuA. MuA binds specific target sites and synapses them together to form the transposon. MuA remains bound until it is disassembled by the ATP-ClpX chaperone (Harshey, 2012). Meanwhile, MuGam binds to excised Mu phage DNA and protects it from digestion by host nucleases. Transposition events promote the uptake of foreign linear DNA: this function is known as natural competence and is linked to horizontal gene transfer (HGT). HGT is the transfer of foreign DNA between organisms and significantly contributes to the spread of antibiotic resistance and evolution in bacteria (Gyles and Boerlin, 2014).

MuGam enables natural competence in E. coli and is therefore a putative agent of HGT. Bacteria possessing a Gam-like prophage region should also be naturally competent. In Haemophilus influenzae, Gam (HiGam) inhibits digestion of Mu phage DNA by nucleases (d’Adda di Fagagna, Weller, Doherty, et al., 2003). Through sequence alignment, we identified and cloned a putative homologue of Mu phage Gam from Haemophilus influenzae (HiGam). The structure – including binding affinity, oligomeric state – of HiGam was assessed in comparison to MuGam in literature. A range of assays were used to achieve this, namely electrophoretic mobility shift assay (EMSA), sodium dodecyl sulphate– polyacrylamide gel electrophoresis (SDS-PAGE) and size exclusion chromatography (SEC). Similarities to Mu will insinuate that HiGam will too function as an agent of horizontal gene transfer.

The aim of this report is to characterise HiGam by processing the data obtained from assays.

2 Requirements

Required software and packages are outlined in the README.

3 The Data

4 Analysis

4.1 Diagnostic PCR of the Mu Prophage Region in Haemophilus influenzae Genomic DNA and cDNA

Diagnostic PCR was used to amplify the H. influenzae homologues, and to test for their transcription relative to the Genomic DNA (gDNA) control. Amplicon sizes were established with equation (1), using DNA ladder molecular weight (MW) standards. Results identified the transcription of HiA, HiB, HiGam, HiA-HiB and HiB-HiGam in H. influenzae (Figure 4.1.1).

\[\begin{equation} \Large \color{#8D9FCA} y \color{#5a5a5a} = \color{#E789C2} m \color{#66c2a4} x \color{#5a5a5a} + \color{#FFD82F} c\\ \small \text{Where } \color{#8D9FCA} y = \text{log(DNA MW in bp), } \color{#E789C2} m = \text{gradient, } \color{#66c2a4} x = \text{Rf, and } \color{#FFD82F} c = \text{y-intercept}\tag{1} \end{equation}\]

4.1.1 Expressed Amplicons

Figure 4.1.1: Expression levels of HiA, HiB and HiGam ORFs in the complementary DNA (cDNA) and genomic DNA (gDNA) libraries, compared to their expected sizes. Results indicate that HiA, HiB and HiGam genes are expressed, and that poly-cistronic transcripts encoding HiA-HiB and HiB-HiGam gene pairs exist in H. influenzae.

4.1.2 Dataset

Library Amplicon Distance (cm) Expected Size (bp) Relative Front (Rf) Log(Rf) Actual Size (bp) Size Difference (%)
gDNA HiA 11.40 157 0.09 2.01 102.19 34.91
HiB 11.04 208 0.12 2.09 122.42 41.15
HiGam 10.77 245 0.14 2.15 140.17 42.79
HiA-HiB 5.27 2122 0.58 3.34 2213.08 -4.29
HiB-HiGam 6.48 1319 0.48 3.08 1206.04 8.56
cDNA HiA 11.77 157 0.06 2.00 100.80 35.80
HiB 11.42 208 0.09 2.08 119.90 42.35
HiGam 10.14 245 0.19 2.35 226.17 7.69
HiA-HiB 5.22 2122 0.58 3.41 2593.09 -22.20
HiB-HiGam 6.46 1319 0.48 3.15 1402.23 -6.31

Table 4.1.2:

4.2 Analyse DNA-Binding Properties of HiGam in EMSA

Electrophoretic mobility shift assay (EMSA) was used to examine whether Im9-HiGam–DNA had an affinity for closed circular DNA or linear DNA. EMSA was performed using purified, recombinant Im9-HiGam, with supercoiled plasmid plasmid DNA and linear DNA templates. A fixed concentration of DNA was used with varying concentrations of Im9-HiGam to saturate binding to DNA. Rf was calculated in R using calculation (2).

\[\begin{equation} \frac{(\text{gel length} - \text{distance})}{\text{gel length}}\tag{2} \end{equation}\]

Im9-HiGam was observed to bind preferentially to linear DNA with a dissociation constant (\(K_D\)) of approximately 0.52M (Figure ??). Results estimate Im9-HiGam has a binding dimeric footprint of approximately 22 base pairs.

4.2.1 Analysis

Figure 4.2.1: The binding affinity (equilibrium dissociation constant, KD) was estimated by nonlinear regression analysis of EMSA using the Langmuir Binding Isotherm.

4.2.2 Dataset

Concentration Distance Relative Front Residuals
0.0 6.20 0.31 0.01
0.5 4.81 0.46 -0.06
1.0 3.20 0.64 0.05
1.5 3.10 0.66 0.02
2.0 3.00 0.67 0.01
3.0 3.00 0.67 -0.01
4.0 3.00 0.67 -0.03

Table 4.2.2:

4.3 Size Exclusion Chromatography (SEC)

Size exclusion chromatography (SEC) was used to explore the molecular weight and oligomeric state of Im9-HiGam. 7 chromatograms of known MW were plotted and a linear regression was performed to determine the relationship between elution volume and molecular weight (Figure 4.3.3). The SEC data showed a peak for both wavelengths, with a MW of approximately 77703.42 Daltons for A254 and 58853.86 Daltons for A280 (Figure 4.3.1). This gives Im9-HiGam has an estimated monomeric footprint of approximately 28.56 base pairs.

4.3.1 Analysis

Figure 4.3.1:

4.3.2 Calibration Plot

Figure 4.3.2:

4.3.3 Standards

Figure 4.3.3:

4.3.4 Dataset

Volume a254 a280
0.00 0.10 0.18
0.02 0.20 0.18
0.05 0.07 -0.01
0.07 -0.04 -0.04
0.10 -0.02 -0.20
0.12 -0.11 0.10
0.14 0.07 -0.09
0.17 -0.03 0.06
0.19 -0.06 -0.36
0.22 0.07 -0.15
0.24 0.14 -0.33
0.26 -0.12 -0.10
0.29 0.19 0.14
0.31 0.02 0.04
0.34 0.05 0.12
0.36 0.03 0.19
0.38 -0.02 -0.32
0.41 0.12 0.21
0.43 -0.13 0.01
0.46 0.08 -0.07
0.48 -0.11 0.15
0.50 -0.06 -0.03
0.53 -0.11 -0.02
0.55 0.01 -0.02
0.58 -0.15 -0.04
0.60 0.10 -0.03
0.62 0.13 -0.12
0.65 -0.17 0.32
0.67 0.05 0.04
0.70 0.19 0.27
0.72 0.12 -0.21
0.74 0.20 -0.25
0.77 0.08 0.06
0.79 -0.14 0.18
0.82 -0.03 0.04
0.84 -0.17 -0.13
0.86 0.10 0.08
0.89 0.07 -0.04
0.91 0.02 0.35
0.94 0.16 -0.02
0.96 0.00 0.09
0.98 0.03 0.01
1.01 -0.10 0.12
1.03 -0.16 -0.23
1.06 0.13 -0.09
1.08 -0.19 -0.04
1.11 0.11 -0.14
1.13 0.03 0.00
1.15 0.04 -0.05
1.18 -0.06 0.01
1.20 -0.18 0.02
1.23 0.05 0.15
1.25 0.01 0.02
1.27 -0.14 -0.27
1.30 0.15 -0.19
1.32 -0.17 -0.29
1.35 -0.02 -0.18
1.37 0.14 -0.15
1.39 0.02 0.10
1.42 -0.06 -0.27
1.44 0.01 0.03
1.47 -0.13 0.05
1.49 0.07 -0.32
1.51 -0.07 -0.21
1.54 -0.15 -0.04
1.56 0.01 -0.02
1.59 -0.01 0.11
1.61 -0.13 -0.16
1.63 0.03 0.19
1.66 0.13 0.19
1.68 -0.18 -0.09
1.71 0.03 0.07
1.73 0.15 -0.02
1.75 0.03 0.14
1.78 -0.01 0.18
1.80 0.14 -0.19
1.83 0.11 0.26
1.85 -0.15 -0.14
1.87 -0.17 -0.24
1.90 0.11 -0.03
1.92 -0.21 0.17
1.95 0.12 0.29
1.97 0.06 -0.28
1.99 0.19 -0.03
2.02 0.15 -0.06
2.04 -0.10 0.21
2.07 -0.21 -0.19
2.09 0.06 0.08
2.11 0.05 -0.02
2.14 0.17 -0.34
2.16 -0.13 -0.24
2.19 0.17 0.10
2.21 -0.10 0.08
2.23 0.06 -0.04
2.26 -0.14 0.00
2.28 0.09 0.10
2.31 -0.04 0.18
2.33 0.03 0.12
2.35 -0.03 0.21
2.38 -0.19 0.06
2.40 0.19 0.33
2.43 -0.06 0.24
2.45 0.12 0.28
2.47 -0.12 0.07
2.50 0.16 0.19
2.52 -0.14 0.21
2.55 0.17 0.02
2.57 -0.07 0.12
2.59 0.17 0.01
2.62 0.14 -0.06
2.64 0.10 0.18
2.67 -0.05 0.17
2.69 0.10 0.03
2.71 0.11 0.24
2.74 -0.10 -0.08
2.76 0.03 -0.03
2.79 0.05 -0.01
2.81 -0.13 0.33
2.83 0.08 0.03
2.86 0.15 -0.02
2.88 -0.02 0.32
2.91 -0.20 0.35
2.93 0.00 -0.07
2.95 0.07 0.18
2.98 -0.12 0.06
3.00 -0.01 0.10
3.03 -0.03 0.06
3.05 -0.14 -0.16
3.08 -0.02 0.13
3.10 0.00 -0.11
3.12 -0.10 -0.20
3.15 -0.13 -0.07
3.17 0.02 -0.13
3.20 0.13 0.21
3.22 0.19 -0.18
3.24 0.14 -0.08
3.27 0.18 0.24
3.29 -0.16 -0.31
3.32 0.05 -0.23
3.34 -0.02 0.05
3.36 -0.02 -0.11
3.39 -0.02 0.12
3.41 0.02 -0.21
3.44 0.04 0.12
3.46 -0.10 0.01
3.48 0.01 0.03
3.51 0.09 0.11
3.53 0.09 -0.03
3.56 0.12 -0.08
3.58 0.19 -0.06
3.60 0.10 0.06
3.63 -0.01 -0.12
3.65 0.19 -0.02
3.68 -0.11 -0.16
3.70 -0.06 -0.08
3.72 -0.03 -0.39
3.75 0.00 -0.11
3.77 -0.07 0.00
3.80 0.11 -0.16
3.82 0.13 -0.07
3.84 0.10 -0.22
3.87 -0.16 -0.20
3.89 0.16 -0.08
3.92 0.06 0.32
3.94 0.11 0.13
3.96 -0.05 -0.12
3.99 -0.17 -0.18
4.01 0.11 -0.04
4.04 -0.02 -0.31
4.06 -0.05 -0.02
4.08 0.11 0.02
4.11 0.13 -0.32
4.13 0.15 -0.16
4.16 0.11 -0.28
4.18 0.03 -0.03
4.20 0.06 0.06
4.23 -0.01 0.15
4.25 -0.03 0.16
4.28 -0.01 0.15
4.30 -0.15 0.07
4.32 0.20 -0.01
4.35 -0.15 -0.15
4.37 -0.02 0.12
4.40 0.16 0.10
4.42 -0.13 -0.23
4.44 -0.05 -0.13
4.47 -0.15 -0.29
4.49 -0.03 0.03
4.52 -0.01 0.07
4.54 -0.03 -0.19
4.56 0.12 -0.04
4.59 -0.20 -0.01
4.61 0.12 0.27
4.64 0.04 -0.21
4.66 -0.12 -0.18
4.68 0.03 -0.15
4.71 -0.08 -0.05
4.73 -0.06 0.09
4.76 -0.06 0.12
4.78 -0.19 -0.01
4.80 0.02 -0.35
4.83 0.02 0.33
4.85 0.09 0.25
4.88 -0.14 -0.10
4.90 0.15 0.18
4.92 0.15 0.12
4.95 -0.10 0.02
4.97 -0.03 -0.07
5.00 -0.05 -0.01
5.02 -0.13 -0.03
5.05 0.04 0.23
5.07 0.09 -0.07
5.09 0.09 -0.06
5.12 0.02 0.04
5.14 -0.15 -0.15
5.17 -0.11 0.02
5.19 -0.03 0.31
5.21 -0.20 0.01
5.24 0.06 -0.15
5.26 0.00 -0.24
5.29 0.09 0.21
5.31 -0.08 0.05
5.33 0.07 -0.12
5.36 0.11 0.09
5.38 -0.12 -0.06
5.41 -0.03 -0.14
5.43 -0.05 -0.03
5.45 0.13 -0.18
5.48 -0.06 -0.03
5.50 0.20 0.15
5.53 -0.05 0.20
5.55 0.05 -0.08
5.57 0.14 0.05
5.60 0.06 -0.12
5.62 -0.12 0.18
5.65 -0.16 0.01
5.67 -0.11 -0.20
5.69 -0.16 -0.28
5.72 -0.11 0.06
5.74 -0.16 -0.20
5.77 -0.07 -0.07
5.79 0.01 -0.01
5.81 0.16 -0.07
5.84 -0.12 0.06
5.86 0.12 0.12
5.89 -0.07 0.19
5.91 0.02 0.27
5.93 -0.10 -0.02
5.96 -0.12 -0.05
5.98 0.18 0.28
6.01 -0.15 0.01
6.03 0.12 -0.07
6.05 -0.16 0.24
6.08 0.02 0.06
6.10 -0.01 0.05
6.13 -0.08 0.25
6.15 0.09 0.24
6.17 -0.01 0.27
6.20 -0.03 -0.16
6.22 0.07 -0.32
6.25 -0.19 -0.04
6.27 -0.19 -0.22
6.29 -0.08 0.22
6.32 0.17 -0.16
6.34 -0.08 0.01
6.37 -0.11 -0.30
6.39 -0.12 0.03
6.41 0.03 -0.29
6.44 -0.12 0.31
6.46 -0.08 0.01
6.49 0.13 0.21
6.51 0.05 -0.06
6.53 0.16 -0.06
6.56 -0.13 -0.12
6.58 0.17 0.33
6.61 0.13 0.00
6.63 0.12 -0.09
6.65 -0.18 -0.06
6.68 0.21 0.33
6.70 0.12 0.31
6.73 -0.11 0.00
6.75 -0.17 0.00
6.77 0.16 0.23
6.80 -0.03 -0.05
6.82 -0.09 0.27
6.85 0.18 0.01
6.87 0.17 -0.27
6.89 -0.09 0.11
6.92 0.01 -0.17
6.94 -0.17 -0.02
6.97 0.19 0.01
6.99 -0.06 0.29
7.02 0.01 0.04
7.04 0.11 -0.17
7.06 0.02 -0.33
7.09 -0.01 -0.15
7.11 -0.07 -0.30
7.14 -0.05 -0.26
7.16 -0.05 -0.04
7.18 -0.12 -0.17
7.21 0.14 -0.10
7.23 -0.08 -0.08
7.26 -0.16 0.21
7.28 -0.03 -0.12
7.30 -0.16 0.13
7.33 0.18 0.12
7.35 -0.19 0.14
7.38 0.00 0.17
7.40 0.08 0.23
7.42 -0.18 0.14
7.45 -0.03 -0.22
7.47 0.04 0.21
7.50 -0.04 0.07
7.52 -0.14 -0.08
7.54 -0.08 0.05
7.57 0.16 0.02
7.59 0.04 -0.08
7.62 0.01 0.27
7.64 -0.17 -0.05
7.66 0.06 0.24
7.69 0.05 -0.05
7.71 0.15 -0.05
7.74 -0.11 0.03
7.76 0.17 0.22
7.78 -0.18 0.31
7.81 -0.04 0.25
7.83 -0.08 -0.34
7.86 -0.19 -0.37
7.88 -0.08 -0.05
7.90 0.17 0.11
7.93 -0.20 0.03
7.95 -0.01 0.22
7.98 0.18 -0.14
8.00 -0.12 -0.06
8.02 0.08 -0.31
8.05 -0.04 -0.23
8.07 0.16 0.01
8.10 -0.18 0.17
8.12 -0.16 -0.13
8.14 0.06 0.21
8.17 0.08 -0.13
8.19 -0.04 0.01
8.22 -0.04 -0.16
8.24 0.15 -0.15
8.26 -0.18 -0.15
8.29 0.06 -0.05
8.31 -0.21 0.24
8.34 0.12 0.03
8.36 0.02 -0.22
8.38 0.10 0.06
8.41 -0.09 0.28
8.43 -0.18 -0.04
8.46 0.03 -0.05
8.48 0.06 -0.18
8.50 0.10 0.07
8.53 0.08 0.31
8.55 -0.03 0.06
8.58 0.19 0.08
8.60 -0.08 0.01
8.62 -0.03 -0.17
8.65 -0.10 -0.12
8.67 -0.17 0.31
8.70 -0.13 -0.17
8.72 0.07 0.22
8.74 -0.08 0.20
8.77 0.22 0.10
8.79 0.12 -0.21
8.82 -0.11 0.07
8.84 -0.02 0.24
8.86 -0.19 0.18
8.89 0.16 -0.08
8.91 0.02 -0.13
8.94 0.17 0.24
8.96 -0.12 0.16
8.98 -0.10 0.13
9.01 -0.12 0.13
9.03 0.01 -0.09
9.06 -0.02 0.15
9.08 -0.10 0.25
9.11 -0.06 0.08
9.13 -0.01 -0.08
9.15 0.05 -0.07
9.18 0.16 0.04
9.20 0.11 -0.36
9.23 0.05 0.01
9.25 -0.10 -0.09
9.27 0.15 -0.06
9.30 -0.19 -0.15
9.32 -0.10 0.21
9.35 -0.13 -0.07
9.37 0.06 -0.21
9.39 0.09 -0.03
9.42 0.19 0.04
9.44 0.15 -0.18
9.47 -0.19 0.03
9.49 0.13 -0.01
9.51 0.09 -0.33
9.54 0.14 0.02
9.56 0.17 0.05
9.59 0.01 -0.17
9.61 0.01 -0.26
9.63 -0.09 0.08
9.66 -0.03 0.16
9.68 -0.06 -0.02
9.71 0.07 -0.01
9.73 -0.04 -0.15
9.75 0.05 0.01
9.78 -0.10 -0.14
9.80 0.00 -0.15
9.83 0.02 -0.05
9.85 0.10 0.06
9.87 -0.07 0.25
9.90 -0.01 0.02
9.92 0.11 -0.01
9.95 -0.16 0.01
9.97 -0.09 -0.03
9.99 0.18 -0.21
10.02 -0.01 -0.05
10.04 0.18 0.08
10.07 0.04 0.11
10.09 -0.12 0.05
10.11 -0.05 0.04
10.14 -0.13 -0.30
10.16 0.08 -0.30
10.19 0.06 -0.33
10.21 0.00 -0.12
10.23 0.16 -0.02
10.26 0.04 0.22
10.28 -0.18 -0.24
10.31 0.00 -0.06
10.33 0.03 -0.16
10.35 -0.13 0.18
10.38 0.14 0.28
10.40 -0.10 0.04
10.43 -0.08 0.37
10.45 0.15 0.20
10.47 0.00 0.00
10.50 0.01 -0.37
10.52 -0.17 -0.14
10.55 0.10 0.13
10.57 0.14 -0.01
10.59 0.06 -0.30
10.62 0.14 -0.20
10.64 0.09 -0.26
10.67 -0.02 0.31
10.69 0.06 -0.29
10.71 -0.04 0.06
10.74 0.17 0.05
10.76 -0.10 0.22
10.79 0.15 0.03
10.81 0.08 0.18
10.83 0.20 -0.02
10.86 0.05 -0.23
10.88 -0.11 -0.01
10.91 -0.10 -0.27
10.93 0.06 -0.22
10.95 -0.07 -0.34
10.98 0.07 -0.30
11.00 -0.16 0.17
11.03 0.15 0.03
11.05 -0.19 -0.06
11.08 -0.09 0.00
11.10 0.05 -0.13
11.12 -0.04 0.10
11.15 0.12 0.07
11.17 -0.15 0.08
11.20 0.08 0.16
11.22 0.18 -0.29
11.24 -0.13 0.29
11.27 0.00 0.35
11.29 0.14 0.15
11.32 0.17 0.11
11.34 0.15 -0.15
11.36 -0.04 0.12
11.39 0.04 -0.15
11.41 0.02 0.03
11.44 -0.09 0.09
11.46 -0.19 0.25
11.48 0.02 -0.25
11.51 0.08 0.15
11.53 0.14 -0.04
11.56 -0.04 -0.19
11.58 0.04 -0.17
11.60 -0.08 -0.08
11.63 0.03 -0.09
11.65 -0.14 0.02
11.68 0.01 0.02
11.70 0.09 0.17
11.72 0.04 0.01
11.75 0.18 0.16
11.77 -0.07 0.12
11.80 -0.14 0.03
11.82 -0.09 -0.12
11.84 0.05 -0.20
11.87 -0.02 -0.04
11.89 0.12 -0.06
11.92 -0.18 0.11
11.94 -0.07 -0.04
11.96 -0.05 -0.04
11.99 0.06 -0.16
12.01 0.05 0.28
12.04 0.21 -0.04
12.06 -0.03 0.23
12.08 0.19 0.03
12.11 0.14 0.20
12.13 -0.01 0.11
12.16 -0.05 0.07
12.18 0.13 -0.08
12.20 0.10 -0.01
12.23 0.10 -0.03
12.25 -0.17 -0.21
12.28 -0.19 -0.25
12.30 -0.05 -0.33
12.32 0.03 -0.24
12.35 0.04 -0.08
12.37 -0.01 0.01
12.40 -0.02 0.06
12.42 -0.01 0.01
12.44 -0.03 -0.07
12.47 -0.12 -0.02
12.49 0.16 0.18
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14.37 0.18 1.73
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14.46 2.56 4.83
14.49 3.95 5.86
14.51 5.78 7.80
14.53 8.70 9.62
14.56 12.19 11.65
14.58 17.27 13.71
14.61 23.22 16.31
14.63 30.75 19.22
14.65 39.16 21.21
14.68 48.40 24.35
14.70 58.13 26.80
14.73 67.83 28.88
14.75 76.94 31.51
14.77 84.94 32.86
14.80 90.78 33.98
14.82 94.07 34.83
14.85 95.20 34.81
14.87 93.11 34.84
14.89 88.61 34.25
14.92 81.84 32.51
14.94 73.54 31.18
14.97 64.28 29.91
14.99 54.65 28.31
15.02 45.39 27.15
15.04 36.74 26.37
15.06 29.31 26.30
15.09 23.31 27.59
15.11 18.60 29.29
15.14 14.85 32.40
15.16 12.24 37.32
15.18 10.72 42.31
15.21 9.92 48.80
15.23 9.85 55.12
15.26 9.50 61.48
15.28 9.94 67.53
15.30 9.92 72.08
15.33 9.95 75.20
15.35 10.25 76.03
15.38 10.08 75.04
15.40 9.57 71.51
15.42 9.36 66.80
15.45 8.75 60.38
15.47 8.00 53.11
15.50 7.17 45.22
15.52 6.24 37.54
15.54 5.53 29.93
15.57 4.41 23.39
15.59 3.64 17.80
15.62 3.11 12.88
15.64 2.57 9.75
15.66 2.00 6.77
15.69 1.39 4.09
15.71 0.99 2.76
15.74 0.98 1.73
15.76 0.69 1.34
15.78 0.55 0.62
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17.25 0.21 -0.19
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17.30 0.10 0.01
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19.60 -0.14 -0.17
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20.40 0.21 -0.29
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22.77 0.02 0.17
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22.82 0.10 0.04
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22.99 -0.13 0.21
23.02 0.06 -0.23
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23.06 0.09 -0.22
23.09 0.05 -0.33
23.11 -0.09 -0.21
23.14 -0.14 -0.03
23.16 -0.17 -0.06
23.18 0.15 -0.20
23.21 0.04 0.05
23.23 0.09 -0.34
23.26 0.19 0.25
23.28 0.20 -0.10
23.30 0.16 -0.18
23.33 0.05 -0.03
23.35 0.06 -0.08
23.38 -0.17 0.19
23.40 -0.09 0.17
23.42 0.03 0.35
23.45 0.14 0.06
23.47 -0.09 0.17
23.50 -0.02 -0.25
23.52 -0.04 0.03
23.54 0.01 0.00
23.57 -0.11 -0.10
23.59 -0.02 0.15
23.62 -0.20 0.15
23.64 -0.11 -0.16
23.66 0.13 0.12
23.69 0.17 -0.14
23.71 -0.13 -0.26
23.74 0.19 0.09
23.76 0.11 -0.04
23.78 -0.16 0.32
23.81 0.19 0.05
23.83 -0.14 0.21
23.86 -0.05 0.13
23.88 0.15 -0.09
23.90 0.17 0.21
23.93 -0.17 0.13
23.95 -0.10 -0.07
23.98 -0.11 0.21
24.00 -0.05 0.02

Figure 4.3.4: ___

This Document: 224
README: 94
Total: 318

Report made with rmarkdown (Allaire, Xie, McPherson, et al., 2021; Xie, Allaire, and Grolemund, 2018; Xie, Dervieux, and Riederer, 2020), RefManageR(McLean, 2020).

Theme is Minty by Bootswatch.

5 Bibliography

Packages

Allaire, J., Y. Xie, J. McPherson, et al. (2021). rmarkdown: Dynamic Documents for R. R package version 2.11. URL: https://CRAN.R-project.org/package=rmarkdown.

McLean, M. W. (2020). RefManageR: Straightforward BibTeX and BibLaTeX Bibliography Management. R package version 1.3.0. URL: https://github.com/ropensci/RefManageR/.

Xie, Y., J. Allaire, and G. Grolemund (2018). R Markdown: The Definitive Guide. ISBN 9781138359338. Boca Raton, Florida: Chapman and Hall/CRC. URL: https://bookdown.org/yihui/rmarkdown.

Xie, Y., C. Dervieux, and E. Riederer (2020). R Markdown Cookbook. ISBN 9780367563837. Boca Raton, Florida: Chapman and Hall/CRC. URL: https://bookdown.org/yihui/rmarkdown-cookbook.

References

d’Adda di Fagagna, F., G. R. Weller, A. J. Doherty, et al. (2003). “The Gam protein of bacteriophage Mu is an orthologue of eukaryotic Ku”. En. In: EMBO reports 4.1, pp. 47-52.

Fuller, J. R. and P. A. Rice (2017). “Target DNA bending by the Mu transpososome promotes careful transposition and prevents its reversal”. In: eLife 6.

Gyles, C. and P. Boerlin (2014). “Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease”. En. In: Veterinary pathology 51.2, pp. 328-340.

Harshey, R. M. (2012). “The Mu story: how a maverick phage moved the field forward”. In: Mobile DNA 3.1.

Shapiro, J. A. (1979). “Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements”. En. In: Proceedings of the National Academy of Sciences of the United States of America 76.4, pp. 1933-1937.